CSC

db_info

db_info num_readings io

This command returns the number of readings in the database.

db_info num_contigs io

This command returns the number of contigs in the database.

db_info t_contig_length io

This command returns the total number of characters in the consensus for all contigs.

db_info t_read_length io

This command returns the total number of bases used in all the readings.

db_info get_read_num io reading_identifier

This command returns the reading number (between 1 and num_contigs) for a specific reading. For instance, to convert the reading name xb64a10.s1 to its reading number we use:

set rnum [db_info get_read_num $io xb64a10.s1]

If the reading name is not found, -1 is returned.

db_info get_contig_num io reading_identifier

This command returns the contig number for a specific reading. The number returned is the number of the contig structure, not the number of the left most reading within this contig. It returns -1 for failure.

db_info chain_left io reading_identifier

This command returns the left most reading number within a contig specified by the reading_identifier. It returns -1 for failure.

db_info longest_contig io

This command returns the contig number (not the left most reading number) of the longest contig in the database.

db_info db_name io

This command returns the name of the database opened with the specified io handle. The name returned includes the version number, so an example result would be TEST.0.